Issue with fMRIPrep Preprocessing of a Functional Scan

I am having some issues with the preprocessing of one of our scans through fMRIPrep. Specifically, we are collecting 1 T1-weighted structural scan, 2 resting-state functional scans, 6 functional scans during a go/no-go task, 1 functional scan during the balloon analogue risk taking (BART) task, and 1 diffusion tensor imaging scan. All of our functional scans are multiband with a TR of 0.8s. I submitted all of these scans for preprocessing through fMRIPrep. This generates all the preprocessed figures on the output file for all of the scans; however, no figures or any other information are created about the BART scan in the output report at all, even though no error is thrown.

The MR acquisition parameters for all of our functional scans are identical, except the duration of each scan. Our resting-state scans last ~6min each, our go/no-go scans last ~6.5min each, and our BART scan is set to last for 20 minutes. However, the actual BART task is self-paced and is usually completed within 10 minutes, so we terminate it manually during data collection ourselves when the task is completed. We have collected data from 2 pilot subjects and 1 actual subject for now, and the BART scan has 617, 654, and 703 timepoints for the 3 subjects compared to 470-495 in our go/no-go scans and 455 in our resting-state scans.

I tried preprocessing our data after deleting all of the scans except the structural scan and the BART scan, as well as after using the fslroi command to reduce the number of timepoints of the BART scan to be identical to the number of timepoints of one of the go/no-go scans (for which the figures are successfully generated after submitting them for preprocessing through fMRIPrep) in case the scan was simply too long to preprocess (i.e., cut number of timepoints in the BART scan from 703 to the first ~470). Again, no information about the BART scan was generated in the output file, and no error was thrown.

I would appreciate your help in figuring out how to resolve this issue.

Hi @cleanthism95,

Welcome to neurostars!

Thank you for describing your problem in detail and listing the steps you’ve already taken to try to resolve the issue.

I have a couple follow up questions to best help you.

  1. What version of fmriprep are you running?
  2. Are you running fmriprep through docker, singularity, or a manual install?
  3. Are the derivatives for BART generated? (or is it just missing in the html report?)
  4. What is the directory structure for your BIDS dataset? (if you’re using linux/mac you may have access to the tree command which can you can copy/paste the output here).


Hi @jdkent,

Thank you for your response and additional questions!:

  1. I am using version 1.5.3 of fMRIPrep.
  2. I am running fMRIPrep through a singularity image.
  3. Yes, the derivatives for the BART are generated (e.g., fMRIPrep generates confounds regressors files, masks, etc.).
  4. The directory structure of my BIDS dataset is {sub} / {ses} / {modality} (i.e., anat, func, and dwi). Thank you for suggesting the tree command - the full BIDS directory structure printed by the tree command is:

β”œβ”€β”€ CHANGES

β”œβ”€β”€ code

β”œβ”€β”€ dataset_description.json

β”œβ”€β”€ derivatives

β”œβ”€β”€ participants.json

β”œβ”€β”€ participants.tsv

β”œβ”€β”€ README

β”œβ”€β”€ sourcedata

└── sub-2002

└── ses-01

β”œβ”€β”€ anat

β”‚ β”œβ”€β”€ sub-2002_ses-01_T1w.json

β”‚ └── sub-2002_ses-01_T1w.nii.gz

β”œβ”€β”€ dwi

β”‚ β”œβ”€β”€ sub-2002_ses-01_acq-AP_dwi.bval

β”‚ β”œβ”€β”€ sub-2002_ses-01_acq-AP_dwi.bvec

β”‚ β”œβ”€β”€ sub-2002_ses-01_acq-AP_dwi.json

β”‚ └── sub-2002_ses-01_acq-AP_dwi.nii.gz

└── func

β”œβ”€β”€ sub-2002_ses-01_task-bart_bold.json

β”œβ”€β”€ sub-2002_ses-01_task-bart_bold.nii.gz

β”œβ”€β”€ sub-2002_ses-01_task-gngregular_run-01_bold.json

β”œβ”€β”€ sub-2002_ses-01_task-gngregular_run-01_bold.nii.gz

β”œβ”€β”€ sub-2002_ses-01_task-gngregular_run-02_bold.json

β”œβ”€β”€ sub-2002_ses-01_task-gngregular_run-02_bold.nii.gz

β”œβ”€β”€ sub-2002_ses-01_task-gngreward_run-01_bold.json

β”œβ”€β”€ sub-2002_ses-01_task-gngreward_run-01_bold.nii.gz

β”œβ”€β”€ sub-2002_ses-01_task-gngreward_run-02_bold.json

β”œβ”€β”€ sub-2002_ses-01_task-gngreward_run-02_bold.nii.gz

β”œβ”€β”€ sub-2002_ses-01_task-gngreward_run-03_bold.json

β”œβ”€β”€ sub-2002_ses-01_task-gngreward_run-03_bold.nii.gz

β”œβ”€β”€ sub-2002_ses-01_task-gngreward_run-04_bold.json

β”œβ”€β”€ sub-2002_ses-01_task-gngreward_run-04_bold.nii.gz

β”œβ”€β”€ sub-2002_ses-01_task-rest_run-01_bold.json

β”œβ”€β”€ sub-2002_ses-01_task-rest_run-01_bold.nii.gz

β”œβ”€β”€ sub-2002_ses-01_task-rest_run-02_bold.json

└── sub-2002_ses-01_task-rest_run-02_bold.nii.gz

I have run a command that validates that the structure is BIDS-compatible, and this structure is identical to the structure of a BIDS directory from a different project in which I have successfully run fMRIPrep.

Thank you,

Thanks for the info, in your case, the answer to question number 1 led to the solution, I’ve actually already encountered this issue here and should be fixed in version 1.5.6 of fmriprep, since this is a patch release, no major changes to the underlying workflow should occur between 1.5.3 and 1.5.6.

Would upgrading your fmriprep installation be a possible option for you?

1 Like

Thank you very much for the helpful links and for your suggestion to upgrade my fMRIPrep version. I just reached out to someone from my lab who will upgrade the fMRIPrep version we use here as soon as possible. I will try preprocessing the data again when we upgrade our installation and let you know how that works.

Thanks again!